Variant report

Variant	rs7208449
Chromosome Location	chr17:46663535-46663536
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAZ	chr17:46662285-46664134	IMR90	lung:	n/a	n/a
2	MTA3	chr17:46662378-46664216	GM12878	blood:	n/a	n/a
3	POLR2A	chr17:46662556-46663563	HCT-116	colon:	n/a	n/a
4	REST	chr17:46662270-46663618	A549	lung:	n/a	chr17:46663350-46663363
5	RAD21	chr17:46662302-46663990	HCT-116	colon:	n/a	chr17:46663448-46663458 chr17:46663122-46663136 chr17:46663448-46663460
6	CTBP2	chr17:46662351-46663925	H1-hESC	embryonic stem cell:	n/a	n/a
7	MAX	chr17:46662547-46663631	A549	lung:	n/a	n/a
8	SP1	chr17:46662262-46663584	A549	lung:	n/a	chr17:46662454-46662468 chr17:46662455-46662464 chr17:46662454-46662464
9	POLR2A	chr17:46662730-46664028	HUVEC	blood vessel:	n/a	n/a
10	CTCF	chr17:46663520-46663670	GM06990	blood:	n/a	n/a
11	CTCF	chr17:46663460-46663610	HEK293	kidney:	n/a	n/a
12	ZNF263	chr17:46662541-46663982	HEK293-T-REx	kidney:	n/a	chr17:46663483-46663492
13	SMC3	chr17:46662280-46663538	SK-N-SH	brain:	n/a	n/a
14	CTCF	chr17:46662294-46663582	SK-N-SH	brain:	n/a	chr17:46662761-46662774 chr17:46663429-46663438
15	E2F6	chr17:46662391-46663725	A549	lung:	n/a	n/a
16	POLR2A	chr17:46662591-46663669	HUVEC	blood vessel:	n/a	n/a
17	E2F6	chr17:46662797-46663571	A549	lung:	n/a	n/a
18	CHD1	chr17:46662335-46676284	IMR90	lung:	n/a	chr17:46662455-46662465 chr17:46670083-46670093 chr17:46669891-46669901
19	SUZ12	chr17:46662649-46665098	NT2-D1	testis:	n/a	n/a
20	POLR2A	chr17:46663140-46663662	U87	brain:	n/a	n/a
21	CTCF	chr17:46663420-46663570	GM12873	blood:	n/a	chr17:46663429-46663438
22	POLR2A	chr17:46662544-46663582	HCT-116	colon:	n/a	n/a
23	FOSL2	chr17:46662359-46663909	A549	lung:	n/a	n/a
24	RELA	chr17:46662733-46663936	GM19099	blood:	n/a	n/a
25	RUNX3	chr17:46662684-46663572	GM12878	blood:	n/a	n/a
26	SIN3AK20	chr17:46662148-46664308	PANC-1	pancreas:	n/a	n/a
27	IRF1	chr17:46662468-46663691	K562	blood:	n/a	chr17:46662978-46662992 chr17:46662974-46662985 chr17:46662976-46662990 chr17:46662970-46662991 chr17:46662975-46662988 chr17:46663079-46663093 chr17:46662974-46662987 chr17:46663602-46663611 chr17:46662975-46662988 chr17:46662975-46662989 chr17:46662980-46662993 chr17:46662974-46662994 chr17:46662975-46662986 chr17:46662975-46662987 chr17:46662972-46662989 chr17:46662980-46662994 chr17:46662972-46662986 chr17:46662975-46662988
28	POLR2A	chr17:46663160-46663564	HUVEC	blood vessel:	n/a	n/a
29	SUZ12	chr17:46662105-46664500	H1-hESC	embryonic stem cell:	n/a	n/a
30	RAD21	chr17:46662235-46663727	HCT-116	colon:	n/a	chr17:46663448-46663458 chr17:46663122-46663136 chr17:46663448-46663460
31	RAD21	chr17:46662149-46663606	A549	lung:	n/a	chr17:46663448-46663458 chr17:46663122-46663136 chr17:46663448-46663460
32	STAT5A	chr17:46662641-46663701	GM12878	blood:	n/a	chr17:46662975-46662986 chr17:46662981-46662992 chr17:46663315-46663323
33	POLR2A	chr17:46662683-46663542	ECC-1	luminal epithelium:	n/a	n/a
34	POLR2A	chr17:46655911-46684927	PANC-1	pancreas:	n/a	n/a
35	CTCF	chr17:46663460-46663610	A549	lung:	n/a	n/a
36	TCF12	chr17:46662035-46663784	A549	lung:	n/a	chr17:46662977-46662984
37	MAFK	chr17:46663407-46663560	HepG2	liver:	n/a	n/a
38	PML	chr17:46662460-46663743	GM12878	blood:	n/a	n/a
39	POLR2A	chr17:46662333-46663778	U87	brain:	n/a	n/a
40	GABPA	chr17:46662785-46663672	A549	lung:	n/a	n/a
41	GABPA	chr17:46662777-46663627	A549	lung:	n/a	n/a
42	SIN3AK20	chr17:46662492-46663545	PANC-1	pancreas:	n/a	n/a
43	MAX	chr17:46662130-46663746	A549	lung:	n/a	n/a
44	CTCF	chr17:46662274-46663702	HCT-116	colon:	n/a	chr17:46662761-46662774 chr17:46663429-46663438
45	EP300	chr17:46662697-46663974	GM12878	blood:	n/a	chr17:46663847-46663863 chr17:46663183-46663199 chr17:46663880-46663896 chr17:46663074-46663088 chr17:46663824-46663833
46	POLR2A	chr17:46663242-46663546	HUVEC	blood vessel:	n/a	n/a
47	POLR2A	chr17:46662418-46663696	U87	brain:	n/a	n/a
48	CTCF	chr17:46663400-46663550	HVMF	connective:	n/a	chr17:46663429-46663438
49	CTCF	chr17:46663400-46663550	HEK293	kidney:	n/a	chr17:46663429-46663438
50	POLR2A	chr17:46645331-46684907	PANC-1	pancreas:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr17:46589537..46591935-chr17:46661739..46663956,2	MCF-7	breast:
2	chr17:46639764..46641981-chr17:46663009..46664957,2	MCF-7	breast:
3	chr17:46572626..46574764-chr17:46662731..46664611,2	MCF-7	breast:
4	chr17:46660229..46663792-chr17:46665732..46668852,4	K562	blood:
5	chr17:46530850..46533321-chr17:46662351..46664282,2	K562	blood:
6	chr17:46569545..46570868-chr17:46662367..46663838,14	MCF-7	breast:
7	chr17:46663028..46666157-chr17:46668975..46671535,3	MCF-7	breast:
8	chr17:46655425..46657433-chr17:46661001..46663692,2	MCF-7	breast:

Variant related genes	Relation type
HOXB-AS3	TF binding region
MIR10A	TF binding region
HOXB3	TF binding region
ENSG00000233101	Chromatin interaction
ENSG00000257178	Chromatin interaction
ENSG00000120093	Chromatin interaction
ENSG00000120075	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:1)

rs_ID	r²[population]
rs62064564	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:21 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833469	chr17:46491849-46709406	Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	349 gene(s)	inside rSNPs	diseases
2	esv3420538	chr17:46504944-46861553	Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	369 gene(s)	inside rSNPs	diseases
3	nsv908577	chr17:46584900-46704536	Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	343 gene(s)	inside rSNPs	diseases
4	nsv908578	chr17:46592413-46698710	Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	335 gene(s)	inside rSNPs	diseases
5	nsv908579	chr17:46592413-46727289	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Enhancers Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	349 gene(s)	inside rSNPs	diseases
6	nsv532113	chr17:46598247-47588570	Genic enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	453 gene(s)	inside rSNPs	diseases
7	esv2758459	chr17:46602673-46836837	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	364 gene(s)	inside rSNPs	diseases
8	esv2758694	chr17:46602673-46836837	Active TSS Bivalent Enhancer Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	364 gene(s)	inside rSNPs	diseases
9	nsv908580	chr17:46609103-46698710	Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	335 gene(s)	inside rSNPs	diseases
10	nsv908581	chr17:46610646-46735520	Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	349 gene(s)	inside rSNPs	diseases
11	nsv575480	chr17:46617019-46684929	Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
12	nsv908582	chr17:46617019-46698710	Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Weak transcription Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
13	nsv908583	chr17:46617019-46704536	Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	342 gene(s)	inside rSNPs	diseases
14	nsv833471	chr17:46617787-46783345	Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	356 gene(s)	inside rSNPs	diseases
15	nsv908584	chr17:46618926-46735520	Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	348 gene(s)	inside rSNPs	diseases
16	nsv457822	chr17:46620402-46698710	Flanking Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
17	nsv575481	chr17:46620402-46698710	Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
18	nsv457823	chr17:46620402-46704536	Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	342 gene(s)	inside rSNPs	diseases
19	nsv575482	chr17:46620402-46704536	Active TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	342 gene(s)	inside rSNPs	diseases
20	nsv457824	chr17:46625519-46693491	Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	332 gene(s)	inside rSNPs	diseases
21	nsv575483	chr17:46625519-46693491	Flanking Active TSS Bivalent Enhancer Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	332 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7208449	HOXB2	cis	Thyroid	GTEx
rs7208449	HOXB2	cis	Whole Blood	GTEx

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46658800-46665800	Transcr. at gene 5' and 3'	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr17:46661600-46667000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr17:46661800-46663800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr17:46661800-46664000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr17:46662000-46663800	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
6	chr17:46662000-46664600	Active TSS	NHDF-Ad	bronchial
7	chr17:46662000-46665200	Active TSS	Colon Smooth Muscle	Colon
8	chr17:46662200-46663600	Active TSS	Esophagus	oesophagus
9	chr17:46662200-46663600	Active TSS	HSMM	muscle
10	chr17:46662200-46664000	Active TSS	Fetal Kidney	kidney
11	chr17:46662200-46664000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
12	chr17:46662200-46664000	Active TSS	Right Atrium	heart
13	chr17:46662200-46664200	Active TSS	Rectal Smooth Muscle	rectum
14	chr17:46662400-46663600	Active TSS	Aorta	Aorta
15	chr17:46662400-46663600	Active TSS	HSMMtube	muscle
16	chr17:46662400-46663800	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr17:46662400-46663800	Flanking Bivalent TSS/Enh	Fetal Intestine Small	intestine
18	chr17:46662400-46663800	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
19	chr17:46662400-46663800	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
20	chr17:46662400-46663800	Active TSS	Psoas Muscle	Psoas
21	chr17:46662400-46664000	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
22	chr17:46662400-46664000	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
23	chr17:46662400-46664000	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr17:46662400-46664000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr17:46662400-46664000	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
26	chr17:46662400-46664000	Flanking Active TSS	Stomach Smooth Muscle	stomach
27	chr17:46662400-46664200	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
28	chr17:46662400-46664200	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
29	chr17:46662400-46664200	Flanking Bivalent TSS/Enh	Fetal Intestine Large	intestine
30	chr17:46662400-46664200	Flanking Active TSS	HUVEC	blood vessel
31	chr17:46662400-46665000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
32	chr17:46662400-46665000	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
33	chr17:46662400-46665600	Flanking Active TSS	Adipose Nuclei	Adipose
34	chr17:46662400-46668000	Flanking Active TSS	Primary hematopoietic stem cells	blood
35	chr17:46662600-46663600	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
36	chr17:46662600-46663600	Flanking Active TSS	Pancreas	Pancrea
37	chr17:46662600-46663800	Flanking Bivalent TSS/Enh	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr17:46662600-46663800	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr17:46662600-46664000	Flanking Bivalent TSS/Enh	Primary T helper cells fromperipheralblood	blood
40	chr17:46662600-46664000	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
41	chr17:46662800-46663600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr17:46662800-46663600	Flanking Bivalent TSS/Enh	Primary neutrophils fromperipheralblood	blood
43	chr17:46662800-46663600	Flanking Bivalent TSS/Enh	Primary B cells from peripheral blood	blood
44	chr17:46662800-46663600	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
45	chr17:46662800-46663600	Active TSS	Ovary	ovary
46	chr17:46662800-46663600	Active TSS	Spleen	Spleen
47	chr17:46662800-46663800	Flanking Bivalent TSS/Enh	Primary monocytes fromperipheralblood	blood
48	chr17:46662800-46663800	Flanking Bivalent TSS/Enh	Primary B cells from cord blood	blood
49	chr17:46662800-46664000	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr17:46662800-46664000	Active TSS	Right Ventricle	heart

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